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Genotype networks in metabolic reaction spaces [article]

Areejit Samal, Joao F. Matias Rodrigues, Jürgen Jost, Olivier C. Martin, Andreas Wagner
2010 arXiv   pre-print
The robustness of metabolic phenotypes to random reaction removal in such spaces has a narrow distribution with a high mean.  ...  We show that regardless of the number of reactions in a metabolic genotype, the genotypes of a given phenotype typically form vast, connected, and unstructured sets -- genotype networks -- that nearly  ...  The metabolic network of any one organism can be thought of as existing in a vast genotype space of possible metabolic networks.  ... 
arXiv:1004.1727v1 fatcat:ui2jspsx7ncqpoki24aefvwwzi

Genotype networks in metabolic reaction spaces

Areejit Samal, Joao F. Matias Rodrigues, Jurgen Jost, Olivier C. Martin, Andreas Wagner
2010 BMC Systems Biology  
The robustness of metabolic phenotypes to random reaction removal in such spaces has a narrow distribution with a high mean.  ...  Conclusions: Our work shows that phenotype-preserving genotype networks have generic organizational properties and that these properties are insensitive to the number of reactions in metabolic genotypes  ...  The metabolic network of any one organism can be thought of as existing in a vast genotype space of possible metabolic networks.  ... 
doi:10.1186/1752-0509-4-30 pmid:20302636 pmcid:PMC2858107 fatcat:ls5medr3wveavhqziihr2wncke

Exhaustive Analysis of a Genotype Space Comprising 1015 Central Carbon Metabolisms Reveals an Organization Conducive to Metabolic Innovation

Sayed-Rzgar Hosseini, Aditya Barve, Andreas Wagner, Christoph Kaleta
2015 PLoS Computational Biology  
Here we study metabolism's potential for innovation by analyzing an exhaustive genotype-phenotype map for a space of 10 15 metabolisms that encodes all possible subsets of 51 reactions in central carbon  ...  Metabolisms with any one phenotype typically form a single network of genotypes that extends far or all the way through metabolic genotype space, where any two genotypes can be reached from each other  ...  networks abut each other in the genotype space.  ... 
doi:10.1371/journal.pcbi.1004329 pmid:26252881 pmcid:PMC4529314 fatcat:rgqjy3q455ctviybclzf7ylxdq

Genotype networks, innovation, and robustness in sulfur metabolism

João F Matias Rodrigues, Andreas Wagner
2011 BMC Systems Biology  
Results: We show that metabolic genotypes with the same phenotype form large connected genotype networks -networks of metabolic networks -that extend far through metabolic genotype space.  ...  A super-essential reaction is an essential reaction that occurs in all networks viable in a given environment.  ...  Because our genotype space has 1221 metabolic reactions, each metabolic network has 1221 neighbors.  ... 
doi:10.1186/1752-0509-5-39 pmid:21385333 pmcid:PMC3060865 fatcat:apf4wda4kbbkpcxgoyuznl6v5e

Genotype networks, innovation, and robustness in sulfur metabolism [article]

João F. Matias Rodrigues, Andreas Wagner
2010 arXiv   pre-print
How far they reach through this space is a linear function of the number of super-essential reactions in such networks, the number of reactions that occur in all networks with the same phenotype.  ...  We show that metabolic genotypes with the same phenotype form large connected genotype networks that extend far through metabolic genotype space.  ...  Because our genotype space has 1221 metabolic reactions, each metabolic network has 1221 neighbors.  ... 
arXiv:1010.0934v1 fatcat:4bwztomrgfg5fdwq6vy2tkipli

Evolutionary Plasticity and Innovations in Complex Metabolic Reaction Networks

João F. Matias Rodrigues, Andreas Wagner, Nathan D. Price
2009 PLoS Computational Biology  
Two such networks typically differ in most of their reactions and have few essential reactions in common.  ...  Using flux balance analysis we study a vast space of metabolic network genotypes and their relationship to metabolic phenotypes, the ability to sustain life in an environment defined by an available spectrum  ...  Any one organism's metabolic network exists in a much larger space of metabolic genotypes. This space is defined by the biochemical reactions known to be realized in living cells.  ... 
doi:10.1371/journal.pcbi.1000613 pmid:20019795 pmcid:PMC2785887 fatcat:ygeidgazlfc4jjglaslpm6qavu

Metabolic Networks and Their Evolution [chapter]

Andreas Wagner
2012 Advances in Experimental Medicine and Biology  
I will discuss here two such changes, namely the elimination of reactions from a metabolic network through loss of function mutations in enzyme-coding genes, and the addition of metabolic reactions, for  ...  for all network reactions.  ...  In this space, one can define a distance between metabolic genotypes as the fraction of metabolic reactions in which these genotypes differ.  ... 
doi:10.1007/978-1-4614-3567-9_2 pmid:22821452 fatcat:yigcpot3srfrnigol5bucqdism

The molecular origins of evolutionary innovations

Andreas Wagner
2011 Trends in Genetics  
Material in this review is a condensed version of a broad theory of innovation presented elsewhere [109] .  ...  Two metabolic networks have a genotype distance D in this space, which can be represented as the fraction of reactions in which they differ.  ...  Starting from a metabolic network with a given phenotype, one can explore metabolic genotype space through random walks in this space.  ... 
doi:10.1016/j.tig.2011.06.002 pmid:21872964 fatcat:k72eu6g2x5fadff7clww34tz4m

Historical contingency and the gradual evolution of metabolic properties in central carbon and genome-scale metabolisms

Aditya Barve, Sayed-Rzgar Hosseini, Olivier C Martin, Andreas Wagner
2014 BMC Systems Biology  
Conclusions: Metabolism is thus highly evolvable, in the sense that its properties could be fine-tuned by successively altering individual reactions.  ...  Results: We here computationally explore two vast spaces of possible metabolisms to ask whether viable metabolisms are connected.  ...  Terrence Oas at Duke University for providing the script for visualization of genotype spaces.  ... 
doi:10.1186/1752-0509-8-48 pmid:24758311 pmcid:PMC4022055 fatcat:25myx2lmovdapjnpzv7jf5g5ym

A Sequence-to-Function Map for Ribozyme-Catalyzed Metabolisms [chapter]

Alexander Ullrich, Christoph Flamm
2011 Lecture Notes in Computer Science  
Further, we successfully apply the mapping in an existing model for the evolution of a ribozyme-catalyzed metabolism.  ...  We introduce a novel genotype-phenotype mapping based on the relation between RNA sequence and its secondary structure for the use in evolutionary studies.  ...  The conjunction of metabolites and their participation in metabolic reactions is captured in the metabolic network.  ... 
doi:10.1007/978-3-642-21314-4_3 fatcat:thpr4iroabcd3biaz722yx2t7m

Environmental versatility promotes modularity in genome-scale metabolic networks [article]

Areejit Samal, Andreas Wagner, Olivier C. Martin
2011 arXiv   pre-print
For such networks, we define a network module as a maximal set of reactions that are fully coupled, i.e., whose fluxes can only vary in fixed proportions.  ...  We here ask whether this last scenario may play a role in genome-scale metabolic networks that need to sustain life in one or more chemical environments.  ...  support through Swiss National Science Foundation grants 315200-116814, 315200-119697, and 315230-129708, as well as through the YeastX project of SystemsX.ch, and the University Priority Research Program in  ... 
arXiv:1108.4951v1 fatcat:qcn74cgfv5emlcr6xywpaqykly

Environmental versatility promotes modularity in genome-scale metabolic networks

Areejit Samal, Andreas Wagner, Olivier C Martin
2011 BMC Systems Biology  
RESULTS: Using recently developed techniques to randomly sample large numbers of viable metabolic networks from a vast space of metabolic networks, we use flux balance analysis to study in silico metabolic  ...  This organizational principle is insensitive to the environments we consider and to the number of reactions in a metabolic network.  ...  support through Swiss National Science Foundation grants 315200-116814, 315200-119697, and 315230-129708, as well as through the YeastX project of SystemsX.ch, and the University Priority Research Program in  ... 
doi:10.1186/1752-0509-5-135 pmid:21864340 pmcid:PMC3184077 fatcat:vi76aluf5rhpfej5wkbryq6lji

Genotype networks shed light on evolutionary constraints

Andreas Wagner
2011 Trends in Ecology & Evolution  
In these systems, genotypes with the same phenotype form large genotype networks that extend throughout a vast genotype space.  ...  In these systems, genotypes with the same phenotype form large genotype networks that extend throughout a vast genotype space.  ...  Some material in this article is expanded on in [53] by the same author.  ... 
doi:10.1016/j.tree.2011.07.001 pmid:21840080 fatcat:gtbeypbtqzeg5cx4bnigo7mo6m

The Role of Randomness in Darwinian Evolution*

Andreas Wagner
2012 Philosophy of Science  
Historically, one of the most controversial aspects of Darwinian evolution has been the prominent role that randomness and random change play in it.  ...  Here I discuss three very different classes of well-studied molecular phenotypes in which mutations cause nonrandom changes, based on our current knowledge.  ...  The genotype space of metabolic networks is the space of all possible metabolic networks.  ... 
doi:10.1086/663239 fatcat:mgkltmf225altjt4ydudqzifxe

Metabolic Pathway Analysis: Basic Concepts and Scientific Applications in the Post-genomic Era

C.H. Schilling, S. Schuster, B.O. Palsson, R. Heinrich
1999 Biotechnology progress (Print)  
Important algebraic concepts used in pathway analysis, such as null space and convex cone, are explained. It is demonstrated how these concepts can be translated into meaningful metabolic concepts.  ...  in the system.  ...  More importantly, one can interpret the capabilities of a metabolic genotype in terms of a set of metabolic pathways that span its null space providing complete coverage of the solution space.  ... 
doi:10.1021/bp990048k pmid:10356246 fatcat:f65k7v66uff4libjbjublhyn5q
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